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- PDB-5uwo: Crystal Structure of Engineered FMRP-1b NES Peptide in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5uwo
TitleCrystal Structure of Engineered FMRP-1b NES Peptide in complex with CRM1-Ran-RanBP1
Components
  • Engineered FMRP-1b peptide
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / HEAT repeat / NES / nuclear export / Karyopherin
Function / homology
Function and homology information


positive regulation of intracellular transport of viral material / negative regulation of mRNA catabolic process / modulation by host of viral RNA genome replication / regulation of neuronal action potential / growth cone filopodium / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / negative regulation of long-term synaptic depression / neuronal ribonucleoprotein granule ...positive regulation of intracellular transport of viral material / negative regulation of mRNA catabolic process / modulation by host of viral RNA genome replication / regulation of neuronal action potential / growth cone filopodium / poly(G) binding / positive regulation of miRNA-mediated gene silencing / negative regulation of miRNA-mediated gene silencing / negative regulation of long-term synaptic depression / neuronal ribonucleoprotein granule / negative regulation of voltage-gated calcium channel activity / regulation of dendritic spine development / messenger ribonucleoprotein complex / dendritic filopodium / MAPK6/MAPK4 signaling / RNA strand annealing activity / chromocenter / non-membrane-bounded organelle assembly / regulation of neurotransmitter secretion / RNA nuclear export complex / filopodium tip / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / : / regulation of filopodium assembly / negative regulation of synaptic vesicle exocytosis / : / Regulation of cholesterol biosynthesis by SREBP (SREBF) / positive regulation of proteasomal protein catabolic process / importin-alpha family protein binding / N6-methyladenosine-containing RNA reader activity / siRNA binding / poly(A) binding / RNA stem-loop binding / U4 snRNA binding / RNA export from nucleus / spindle pole body / regulatory ncRNA-mediated gene silencing / protein localization to kinetochore / nuclear export / glutamate receptor signaling pathway / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / sequence-specific mRNA binding / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / GTP metabolic process / miRNA binding / poly(U) RNA binding / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / positive regulation of dendritic spine development / positive regulation of filopodium assembly / nuclear import signal receptor activity / regulation of alternative mRNA splicing, via spliceosome / DNA metabolic process / NLS-bearing protein import into nucleus / dynein intermediate chain binding / dynein complex binding / intracellular non-membrane-bounded organelle / dendritic spine neck / ribosomal subunit export from nucleus / spermatid development / mitotic sister chromatid segregation / glial cell projection / ribosomal small subunit export from nucleus / positive regulation of receptor internalization / translation regulator activity / chromosome, centromeric region / ribosomal large subunit export from nucleus / mRNA transport / U5 snRNA binding / sperm flagellum / Cajal body / U2 snRNA binding / negative regulation of cytoplasmic translation / U6 snRNA binding / mRNA export from nucleus / signaling adaptor activity / axon terminus / stress granule assembly / translation initiation factor binding / nuclear pore / U1 snRNA binding / negative regulation of translational initiation / translation repressor activity / methylated histone binding / regulation of mRNA stability / protein export from nucleus / centriole / viral process / molecular condensate scaffold activity / GTPase activator activity / mitotic spindle organization / G protein activity / RNA splicing
Similarity search - Function
Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / : / : / : / : / Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core / Fragile X messenger ribonucleoprotein 1 / Synaptic functional regulator FMRP, KH0 domain / FMR1, tudor domain ...Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / : / : / : / : / Fragile X messenger ribonucleoprotein 1, C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core / Fragile X messenger ribonucleoprotein 1 / Synaptic functional regulator FMRP, KH0 domain / FMR1, tudor domain / Fragile X-related 1 protein core C terminal / FMRP KH0 domain / Fragile X messenger ribonucleoprotein 1, Tudor domain / Agenet-like domain profile. / Agenet-like domain / Agenet domain / Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / K Homology domain / K homology RNA-binding domain / Armadillo-like helical / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Exportin-1 / Ran-specific GTPase-activating protein 1 / GTP-binding nuclear protein Ran / Fragile X messenger ribonucleoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.347 Å
AuthorsFung, H.Y.J. / Chook, Y.M.
Funding support United States, Hong Kong, 7items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)International Student Research Fellowship United States
Croucher FoundationPredoc Research Scholarship Hong Kong
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069909 United States
Welch FoundationI-1532 United States
Leukemia & Lymphoma SocietyScholar Award United States
University of Texas Southwestern Medical CenterEndowed Scholars Program United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP120352, RP150053 United States
CitationJournal: Elife / Year: 2017
Title: Nuclear export receptor CRM1 recognizes diverse conformations in nuclear export signals.
Authors: Fung, H.Y. / Fu, S.C. / Chook, Y.M.
History
DepositionFeb 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: Ran-specific GTPase-activating protein 1
C: Exportin-1
D: Engineered FMRP-1b peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,7768
Polymers163,0464
Non-polymers7314
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10820 Å2
ΔGint-52 kcal/mol
Surface area57570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.475, 106.475, 304.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-1562-

HOH

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 26758.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62826
#2: Protein Ran-specific GTPase-activating protein 1 / Chromosome stability protein 20 / Perinuclear array-localized protein / Ran-binding protein 1 / RANBP1


Mass: 16521.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Plasmid: pGEX-4T3-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41920
#3: Protein Exportin-1 / Karyopherin / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 117458.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGEX-4T3-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30822

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Engineered FMRP-1b peptide


Mass: 2306.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FMRP / Plasmid: pMal-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06787*PLUS

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Non-polymers , 4 types, 549 molecules

#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 16% PEG3350, 100 mM Bis-Tris, pH 6.4, 200 mM ammonium nitrate, 12 mM HCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 74260 / % possible obs: 100 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.039 / Net I/σ(I): 19
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3658 / CC1/2: 0.444 / Rpim(I) all: 0.571 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HB2

4hb2


Resolution: 2.347→40.071 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 2000 2.94 %
Rwork0.1875 --
obs0.1886 67933 91.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.347→40.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10852 0 12 545 11409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311156
X-RAY DIFFRACTIONf_angle_d0.59715112
X-RAY DIFFRACTIONf_dihedral_angle_d15.5176779
X-RAY DIFFRACTIONf_chiral_restr0.0381722
X-RAY DIFFRACTIONf_plane_restr0.0031921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3469-2.40560.2989530.26491744X-RAY DIFFRACTION34
2.4056-2.47060.3295920.25373057X-RAY DIFFRACTION61
2.4706-2.54330.25461380.23954545X-RAY DIFFRACTION90
2.5433-2.62540.2551490.22864898X-RAY DIFFRACTION97
2.6254-2.71920.28191530.2285059X-RAY DIFFRACTION100
2.7192-2.82810.26571540.21525083X-RAY DIFFRACTION100
2.8281-2.95670.21351550.20765100X-RAY DIFFRACTION100
2.9567-3.11260.26211540.20625074X-RAY DIFFRACTION100
3.1126-3.30750.23561550.20285114X-RAY DIFFRACTION100
3.3075-3.56270.22561560.18515138X-RAY DIFFRACTION100
3.5627-3.9210.20081560.1695152X-RAY DIFFRACTION100
3.921-4.48770.19731580.14925206X-RAY DIFFRACTION100
4.4877-5.65150.18411600.15795261X-RAY DIFFRACTION100
5.6515-40.07680.20621670.17835502X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4846-0.44380.07330.51710.42642.14740.02510.02220.1214-0.1510.1472-0.7491-0.30890.3697-0.08840.132-0.0635-0.00620.242-0.13640.51818.014444.430737.9524
20.8341-0.74760.21071.60640.35930.8176-0.07710.3786-0.2662-0.4320.1955-0.4106-0.13170.4607-0.16010.2266-0.07270.12490.3773-0.12520.40467.297246.416525.2192
31.3466-1.4807-0.49494.55121.17752.10490.1860.10780.0179-0.110.1339-1.0599-0.42430.5169-0.31180.258-0.12370.07260.378-0.10030.527711.826353.020838.1184
40.98340.44580.58971.3884-0.51972.80990.06550.016-0.5677-0.17030.081-0.50160.54640.1702-0.08440.15770.01360.00280.3443-0.16020.667811.293632.503334.9883
50.9746-0.1853-0.48811.7252-0.5281.28240.1173-0.001-0.3598-0.06770.0948-0.48590.12290.2283-0.17160.09850.0088-0.01540.1925-0.07740.30990.668237.164939.0922
62.8845-0.41341.65361.8620.03263.8612-0.2363-0.0526-0.01470.2724-0.0853-0.2116-0.24570.11940.33230.1169-0.019-0.03060.1738-0.05860.30261.522943.452143.9293
71.47350.3065-0.47121.543-0.51475.5790.11380.09080.083-0.1966-0.01280.08290.1297-0.7976-0.12220.15710.0456-0.03470.2674-0.06380.2606-11.285341.396234.7168
81.3697-0.37610.15831.20280.08541.7160.1319-0.110.1179-0.0260.0356-0.0924-0.3713-0.0275-0.08310.15690.01020.00970.1557-0.04680.2121-1.739152.008738.243
90.325-0.0650.29830.8312-0.25540.21750.12340.32960.0662-0.26960.1479-0.2927-0.72150.731-0.32480.6316-0.28540.11340.7417-0.12030.535114.033465.283320.2367
100.9022-0.7180.36581.60340.41150.63860.0306-0.0270.01940.18780.27880.17790.0163-0.2018-0.27730.4103-0.10480.17420.4788-0.00680.6041-1.521556.364612.2417
110.17340.06410.11440.02340.01270.08330.2392-0.0790.32640.02580.1127-0.0816-0.2120.192-0.29150.9126-0.21480.08710.80760.07190.62882.248482.728950.5967
121.04170.67920.59821.68840.45841.50490.1125-0.21980.26370.19460.1636-0.1602-0.53920.5675-0.21080.5102-0.17390.20150.3857-0.06250.58756.036366.332318.4038
131.07580.32780.40710.9085-0.43820.6076-0.03420.11970.0808-0.31390.123-0.1713-0.71030.7443-0.0250.7121-0.26350.25940.4469-0.0330.50037.881769.359822.9315
141.46691.06670.11792.62081.49131.128-0.04180.00360.2756-0.38090.1075-0.0763-1.06880.6846-0.03660.6941-0.2540.17410.4732-0.00520.47897.646370.271312.3899
151.713-0.2136-0.20222.36030.72591.408-0.0415-0.2352-0.14290.67510.2572-0.83890.43890.4109-0.14220.2670.1362-0.26460.3128-0.07240.56188.089425.472453.6889
161.3961-0.71140.59071.5978-0.692.97880.05110.0910.09340.02160.04510.0247-0.3035-0.3338-0.09740.19460.01620.03030.2719-0.06460.1326-26.472354.310548.567
172.4186-1.1489-0.77111.93960.53172.24570.09320.1270.2347-0.18250.1524-0.0313-0.6653-0.3515-0.2270.37720.10950.07470.36390.06520.1641-26.398155.71134.3057
180.9456-0.98931.23461.4576-1.88342.57720.1790.131-0.3586-0.15250.09070.27360.17710.0037-0.25160.190.01520.03120.2409-0.09390.3156-8.829517.343814.7068
190.8962-0.6505-0.09220.47120.03430.85580.10040.1130.2651-0.14160.00080.0022-0.1899-0.0112-0.13731.42070.42740.19260.69230.0781.0026-35.504677.216326.7898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 80 )
5X-RAY DIFFRACTION5chain 'A' and (resid 81 through 111 )
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 122 )
7X-RAY DIFFRACTION7chain 'A' and (resid 123 through 142 )
8X-RAY DIFFRACTION8chain 'A' and (resid 143 through 169 )
9X-RAY DIFFRACTION9chain 'A' and (resid 170 through 206 )
10X-RAY DIFFRACTION10chain 'A' and (resid 207 through 216 )
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 82 )
12X-RAY DIFFRACTION12chain 'B' and (resid 83 through 100 )
13X-RAY DIFFRACTION13chain 'B' and (resid 101 through 139 )
14X-RAY DIFFRACTION14chain 'B' and (resid 140 through 199 )
15X-RAY DIFFRACTION15chain 'C' and (resid 0 through 268 )
16X-RAY DIFFRACTION16chain 'C' and (resid 269 through 569 )
17X-RAY DIFFRACTION17chain 'C' and (resid 570 through 808 )
18X-RAY DIFFRACTION18chain 'C' and (resid 809 through 1053 )
19X-RAY DIFFRACTION19chain 'D' and (resid 11 through 20 )

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